Starting phenix.real_space_refine on Sat May 10 17:35:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.map" model { file = "/net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dun_47171/05_2025/9dun_47171.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4309 2.51 5 N 1133 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6672 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2041 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 22, 'TRANS': 238} Chain breaks: 7 Chain: "B" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 22, 'TRANS': 235} Chain breaks: 7 Chain: "C" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1032 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 258 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain breaks: 2 Chain: "F" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain breaks: 1 Time building chain proxies: 4.35, per 1000 atoms: 0.65 Number of scatterers: 6672 At special positions: 0 Unit cell: (83.391, 131.043, 69.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1180 8.00 N 1133 7.00 C 4309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 886.2 milliseconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 38.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.782A pdb=" N ASN A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.669A pdb=" N HIS A 364 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.713A pdb=" N LYS A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.749A pdb=" N ASP A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 532 removed outlier: 3.589A pdb=" N GLN A 532 " --> pdb=" O SER A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 532' Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.644A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 570 " --> pdb=" O THR A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 628 through 633 removed outlier: 4.205A pdb=" N ARG A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.509A pdb=" N LEU A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 removed outlier: 3.876A pdb=" N ASN B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.867A pdb=" N LYS B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.531A pdb=" N SER B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 524 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.578A pdb=" N VAL B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 removed outlier: 4.324A pdb=" N ARG B 633 " --> pdb=" O PRO B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 removed outlier: 3.574A pdb=" N LEU B 650 " --> pdb=" O PRO B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 4.288A pdb=" N PHE C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.037A pdb=" N SER C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.730A pdb=" N LYS C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.766A pdb=" N GLU C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 184 removed outlier: 3.598A pdb=" N CYS C 169 " --> pdb=" O HIS C 165 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 178 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.637A pdb=" N VAL D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR D 55 " --> pdb=" O TRP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.983A pdb=" N SER D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.554A pdb=" N LYS D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.591A pdb=" N LEU D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 161 removed outlier: 3.805A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 184 removed outlier: 3.871A pdb=" N ASP D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.536A pdb=" N VAL A 330 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 349 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 370 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.311A pdb=" N ALA A 556 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 640 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG A 558 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 637 " --> pdb=" O CYS A 581 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 639 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 576 " --> pdb=" O CYS A 611 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 611 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 301 through 303 removed outlier: 3.524A pdb=" N VAL B 330 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.696A pdb=" N LYS B 370 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 559 removed outlier: 6.294A pdb=" N ALA B 556 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 640 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 558 " --> pdb=" O VAL B 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 577 through 578 168 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2103 1.34 - 1.46: 1359 1.46 - 1.58: 3298 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6826 Sorted by residual: bond pdb=" CA ILE A 559 " pdb=" CB ILE A 559 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 7.85e-01 bond pdb=" N PRO A 628 " pdb=" CA PRO A 628 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.14e-01 bond pdb=" CA ASN B 592 " pdb=" CB ASN B 592 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.66e-01 bond pdb=" CB PRO F 651 " pdb=" CG PRO F 651 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.98e-01 bond pdb=" CA HIS C 63 " pdb=" C HIS C 63 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.48e-01 ... (remaining 6821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 8817 1.18 - 2.37: 354 2.37 - 3.55: 92 3.55 - 4.73: 18 4.73 - 5.91: 4 Bond angle restraints: 9285 Sorted by residual: angle pdb=" N ILE C 95 " pdb=" CA ILE C 95 " pdb=" C ILE C 95 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N LEU B 596 " pdb=" CA LEU B 596 " pdb=" C LEU B 596 " ideal model delta sigma weight residual 110.24 114.25 -4.01 1.30e+00 5.92e-01 9.51e+00 angle pdb=" N ILE A 518 " pdb=" CA ILE A 518 " pdb=" C ILE A 518 " ideal model delta sigma weight residual 111.58 108.32 3.26 1.06e+00 8.90e-01 9.48e+00 angle pdb=" C ASP D 61 " pdb=" N ASP D 62 " pdb=" CA ASP D 62 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" C ILE B 595 " pdb=" N LEU B 596 " pdb=" CA LEU B 596 " ideal model delta sigma weight residual 120.82 124.33 -3.51 1.47e+00 4.63e-01 5.69e+00 ... (remaining 9280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 3394 17.16 - 34.33: 434 34.33 - 51.49: 188 51.49 - 68.65: 36 68.65 - 85.82: 11 Dihedral angle restraints: 4063 sinusoidal: 1630 harmonic: 2433 Sorted by residual: dihedral pdb=" CA CYS C 60 " pdb=" C CYS C 60 " pdb=" N ASP C 61 " pdb=" CA ASP C 61 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR B 625 " pdb=" C THR B 625 " pdb=" N PRO B 626 " pdb=" CA PRO B 626 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA CYS D 60 " pdb=" C CYS D 60 " pdb=" N ASP D 61 " pdb=" CA ASP D 61 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 588 0.028 - 0.056: 333 0.056 - 0.085: 93 0.085 - 0.113: 52 0.113 - 0.141: 14 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ILE B 643 " pdb=" N ILE B 643 " pdb=" C ILE B 643 " pdb=" CB ILE B 643 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA VAL B 627 " pdb=" N VAL B 627 " pdb=" C VAL B 627 " pdb=" CB VAL B 627 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CB ILE A 595 " pdb=" CA ILE A 595 " pdb=" CG1 ILE A 595 " pdb=" CG2 ILE A 595 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1077 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 661 " -0.041 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PRO F 662 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 662 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 662 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 625 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 626 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 627 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO A 628 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " 0.020 5.00e-02 4.00e+02 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1345 2.78 - 3.31: 5854 3.31 - 3.84: 10407 3.84 - 4.37: 11885 4.37 - 4.90: 21207 Nonbonded interactions: 50698 Sorted by model distance: nonbonded pdb=" O SER A 427 " pdb=" OG SER A 427 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 636 " pdb=" N ALA F 637 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 571 " pdb=" O ALA D 44 " model vdw 2.252 3.040 nonbonded pdb=" NZ LYS B 312 " pdb=" O THR B 407 " model vdw 2.256 3.120 nonbonded pdb=" NH1 ARG C 121 " pdb=" O LEU D 158 " model vdw 2.271 3.120 ... (remaining 50693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 299 through 408 or resid 420 through 435 or resid 494 thro \ ugh 654)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 41 through 185) } ncs_group { reference = (chain 'E' and resid 636 through 674) selection = (chain 'F' and (resid 636 through 644 or resid 647 through 655 or resid 663 thro \ ugh 674)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6826 Z= 0.126 Angle : 0.593 5.914 9285 Z= 0.316 Chirality : 0.041 0.141 1080 Planarity : 0.005 0.063 1149 Dihedral : 18.866 85.818 2479 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.63 % Allowed : 31.61 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.29), residues: 784 helix: -1.47 (0.30), residues: 265 sheet: -0.87 (0.55), residues: 89 loop : -2.18 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 647 HIS 0.006 0.001 HIS B 364 PHE 0.013 0.002 PHE B 394 TYR 0.011 0.001 TYR B 383 ARG 0.004 0.000 ARG C 171 Details of bonding type rmsd hydrogen bonds : bond 0.21650 ( 168) hydrogen bonds : angle 8.40560 ( 495) covalent geometry : bond 0.00286 ( 6826) covalent geometry : angle 0.59271 ( 9285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 316 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5928 (m-40) REVERT: A 339 GLN cc_start: 0.8087 (mp10) cc_final: 0.7561 (mt0) REVERT: A 369 GLN cc_start: 0.7330 (tt0) cc_final: 0.6955 (mt0) REVERT: A 391 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6852 (mmmt) REVERT: A 419 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3176 (pt) REVERT: A 517 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7400 (tmtt) REVERT: A 610 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6870 (mm) REVERT: B 339 GLN cc_start: 0.8138 (mp10) cc_final: 0.7610 (mt0) REVERT: B 369 GLN cc_start: 0.7160 (tt0) cc_final: 0.6885 (mt0) REVERT: B 383 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: B 391 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6875 (mmmt) REVERT: B 520 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6765 (mtp-110) REVERT: C 162 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7629 (mtpt) REVERT: D 48 ARG cc_start: 0.7096 (mmt90) cc_final: 0.6561 (mmt180) REVERT: D 83 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 162 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7795 (mtpt) REVERT: D 179 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.4677 (t60) REVERT: E 666 MET cc_start: 0.7337 (mmm) cc_final: 0.6891 (mmm) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.2012 time to fit residues: 37.0931 Evaluate side-chains 134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 316 ASN B 385 ASN B 549 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.221730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.193522 restraints weight = 6650.147| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.82 r_work: 0.3965 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6826 Z= 0.107 Angle : 0.563 6.080 9285 Z= 0.289 Chirality : 0.041 0.148 1080 Planarity : 0.005 0.051 1149 Dihedral : 8.756 57.947 964 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.82 % Allowed : 30.69 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.30), residues: 784 helix: -1.02 (0.30), residues: 293 sheet: -0.66 (0.52), residues: 93 loop : -2.38 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 179 HIS 0.006 0.001 HIS B 364 PHE 0.013 0.001 PHE A 362 TYR 0.013 0.001 TYR B 383 ARG 0.005 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 168) hydrogen bonds : angle 5.63520 ( 495) covalent geometry : bond 0.00242 ( 6826) covalent geometry : angle 0.56299 ( 9285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.736 Fit side-chains REVERT: A 339 GLN cc_start: 0.7973 (mp10) cc_final: 0.7358 (mt0) REVERT: A 369 GLN cc_start: 0.7342 (tt0) cc_final: 0.6928 (mt0) REVERT: A 383 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: A 391 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6585 (mmmt) REVERT: A 517 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7245 (tmtt) REVERT: B 339 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: B 369 GLN cc_start: 0.7208 (tt0) cc_final: 0.6953 (mt0) REVERT: B 520 ARG cc_start: 0.7083 (mtm110) cc_final: 0.6633 (mtp-110) REVERT: B 592 ASN cc_start: 0.5637 (t0) cc_final: 0.5422 (t0) REVERT: C 50 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7170 (mt-10) REVERT: C 162 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7473 (mtpt) REVERT: D 83 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7708 (mt-10) REVERT: D 162 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7467 (mtpt) REVERT: D 179 TRP cc_start: 0.5881 (OUTLIER) cc_final: 0.4786 (t60) REVERT: E 666 MET cc_start: 0.7362 (mmm) cc_final: 0.6919 (mmm) outliers start: 44 outliers final: 22 residues processed: 143 average time/residue: 0.1799 time to fit residues: 34.4558 Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 54 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 636 ASN B 385 ASN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.217404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.189148 restraints weight = 6798.882| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.82 r_work: 0.3919 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6826 Z= 0.135 Angle : 0.583 6.335 9285 Z= 0.296 Chirality : 0.042 0.157 1080 Planarity : 0.005 0.059 1149 Dihedral : 8.378 58.952 939 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 5.42 % Allowed : 31.35 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.29), residues: 784 helix: -0.92 (0.30), residues: 288 sheet: -0.43 (0.54), residues: 87 loop : -2.47 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.007 0.001 HIS B 364 PHE 0.014 0.002 PHE A 362 TYR 0.015 0.001 TYR A 332 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 168) hydrogen bonds : angle 5.21095 ( 495) covalent geometry : bond 0.00329 ( 6826) covalent geometry : angle 0.58328 ( 9285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.749 Fit side-chains REVERT: A 339 GLN cc_start: 0.7969 (mp10) cc_final: 0.7388 (mt0) REVERT: A 369 GLN cc_start: 0.7368 (tt0) cc_final: 0.6960 (mt0) REVERT: A 383 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: A 391 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6174 (mmtt) REVERT: A 517 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7301 (tmtt) REVERT: A 519 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7211 (mp) REVERT: B 339 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: B 369 GLN cc_start: 0.7239 (tt0) cc_final: 0.6965 (mt0) REVERT: B 520 ARG cc_start: 0.7112 (mtm110) cc_final: 0.6668 (mtp-110) REVERT: C 50 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 162 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7480 (mtpt) REVERT: C 174 TYR cc_start: 0.6103 (m-80) cc_final: 0.5901 (m-80) REVERT: D 83 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7724 (mt-10) REVERT: D 162 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7431 (mtpt) REVERT: D 179 TRP cc_start: 0.5919 (OUTLIER) cc_final: 0.4802 (t60) REVERT: F 671 ASP cc_start: 0.6641 (t0) cc_final: 0.6437 (t0) outliers start: 41 outliers final: 25 residues processed: 136 average time/residue: 0.1683 time to fit residues: 31.3232 Evaluate side-chains 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 549 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.217410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.188946 restraints weight = 6805.494| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.83 r_work: 0.3918 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6826 Z= 0.127 Angle : 0.571 6.290 9285 Z= 0.290 Chirality : 0.043 0.153 1080 Planarity : 0.005 0.060 1149 Dihedral : 8.315 58.801 937 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 5.82 % Allowed : 30.95 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.29), residues: 784 helix: -0.86 (0.30), residues: 289 sheet: -0.31 (0.56), residues: 87 loop : -2.49 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 577 HIS 0.006 0.001 HIS B 364 PHE 0.014 0.002 PHE D 59 TYR 0.014 0.001 TYR A 332 ARG 0.005 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 168) hydrogen bonds : angle 5.01509 ( 495) covalent geometry : bond 0.00311 ( 6826) covalent geometry : angle 0.57093 ( 9285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.735 Fit side-chains REVERT: A 339 GLN cc_start: 0.7932 (mp10) cc_final: 0.7337 (mt0) REVERT: A 369 GLN cc_start: 0.7276 (tt0) cc_final: 0.6877 (mt0) REVERT: A 383 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: A 391 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6189 (mmtt) REVERT: A 517 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7415 (tmtt) REVERT: A 519 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7197 (mp) REVERT: B 339 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: B 369 GLN cc_start: 0.7139 (tt0) cc_final: 0.6878 (mt0) REVERT: B 520 ARG cc_start: 0.7138 (mtm110) cc_final: 0.6689 (mtp-110) REVERT: B 558 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7030 (ttt90) REVERT: C 50 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7253 (mt-10) REVERT: C 162 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7601 (mtpt) REVERT: D 162 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7463 (mtpt) REVERT: D 170 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6753 (mtt180) REVERT: D 179 TRP cc_start: 0.5950 (OUTLIER) cc_final: 0.4848 (t60) outliers start: 44 outliers final: 29 residues processed: 139 average time/residue: 0.1753 time to fit residues: 32.6749 Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.214492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.186878 restraints weight = 6930.258| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.85 r_work: 0.3885 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6826 Z= 0.175 Angle : 0.629 6.440 9285 Z= 0.318 Chirality : 0.044 0.169 1080 Planarity : 0.006 0.064 1149 Dihedral : 8.701 59.796 937 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.35 % Favored : 88.52 % Rotamer: Outliers : 7.01 % Allowed : 29.76 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.29), residues: 784 helix: -1.04 (0.29), residues: 290 sheet: -0.46 (0.56), residues: 86 loop : -2.65 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 179 HIS 0.008 0.001 HIS B 364 PHE 0.015 0.002 PHE A 362 TYR 0.016 0.002 TYR B 383 ARG 0.004 0.000 ARG A 435 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 168) hydrogen bonds : angle 5.05603 ( 495) covalent geometry : bond 0.00429 ( 6826) covalent geometry : angle 0.62882 ( 9285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.8012 (mp10) cc_final: 0.7388 (mt0) REVERT: A 369 GLN cc_start: 0.7329 (tt0) cc_final: 0.6867 (mt0) REVERT: A 371 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.6089 (tpp) REVERT: A 383 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: A 391 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6344 (mmtt) REVERT: A 517 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7594 (tmtt) REVERT: A 519 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 339 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: B 369 GLN cc_start: 0.7166 (tt0) cc_final: 0.6862 (mt0) REVERT: B 371 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.6280 (tpp) REVERT: B 520 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6808 (mtp-110) REVERT: B 558 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7137 (ttt90) REVERT: C 162 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7689 (mtpt) REVERT: D 162 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7525 (mtpt) REVERT: D 179 TRP cc_start: 0.5981 (OUTLIER) cc_final: 0.4846 (t60) outliers start: 53 outliers final: 33 residues processed: 153 average time/residue: 0.1771 time to fit residues: 36.5746 Evaluate side-chains 147 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.216912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.189536 restraints weight = 6842.270| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.78 r_work: 0.3913 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6826 Z= 0.124 Angle : 0.578 6.131 9285 Z= 0.295 Chirality : 0.042 0.155 1080 Planarity : 0.006 0.067 1149 Dihedral : 8.519 58.871 935 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.33 % Favored : 89.54 % Rotamer: Outliers : 5.82 % Allowed : 30.69 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.29), residues: 784 helix: -0.83 (0.30), residues: 289 sheet: -0.55 (0.55), residues: 87 loop : -2.56 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 179 HIS 0.007 0.001 HIS B 430 PHE 0.016 0.002 PHE B 434 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 168) hydrogen bonds : angle 4.84758 ( 495) covalent geometry : bond 0.00302 ( 6826) covalent geometry : angle 0.57797 ( 9285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7993 (mp10) cc_final: 0.7375 (mt0) REVERT: A 369 GLN cc_start: 0.7303 (tt0) cc_final: 0.6933 (mt0) REVERT: A 383 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: A 391 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6334 (mmtt) REVERT: A 517 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7558 (tmtt) REVERT: A 519 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7376 (mp) REVERT: B 339 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: B 369 GLN cc_start: 0.7144 (tt0) cc_final: 0.6889 (mt0) REVERT: B 408 MET cc_start: 0.7684 (mtt) cc_final: 0.7336 (mtt) REVERT: B 520 ARG cc_start: 0.7182 (mtm110) cc_final: 0.6744 (mtp-110) REVERT: B 558 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7120 (ttt90) REVERT: C 150 TRP cc_start: 0.7843 (t-100) cc_final: 0.7093 (t60) REVERT: C 162 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: D 162 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7533 (mtpt) REVERT: D 179 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.4862 (t60) outliers start: 44 outliers final: 31 residues processed: 140 average time/residue: 0.1921 time to fit residues: 35.8370 Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.215769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.186379 restraints weight = 6877.890| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.92 r_work: 0.3889 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.142 Angle : 0.595 6.943 9285 Z= 0.302 Chirality : 0.043 0.163 1080 Planarity : 0.006 0.065 1149 Dihedral : 8.454 58.000 935 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.84 % Favored : 89.03 % Rotamer: Outliers : 6.48 % Allowed : 29.63 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.29), residues: 784 helix: -0.82 (0.30), residues: 289 sheet: -0.49 (0.57), residues: 86 loop : -2.57 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 179 HIS 0.006 0.001 HIS B 364 PHE 0.019 0.002 PHE B 434 TYR 0.013 0.002 TYR B 383 ARG 0.003 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 168) hydrogen bonds : angle 4.84130 ( 495) covalent geometry : bond 0.00349 ( 6826) covalent geometry : angle 0.59540 ( 9285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7961 (mp10) cc_final: 0.7359 (mt0) REVERT: A 371 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.6092 (tpp) REVERT: A 383 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: A 391 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6177 (mmtt) REVERT: A 517 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7483 (tmtt) REVERT: A 519 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 558 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7023 (ttt90) REVERT: B 339 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: B 369 GLN cc_start: 0.7179 (tt0) cc_final: 0.6847 (mt0) REVERT: B 371 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.6323 (tpp) REVERT: B 408 MET cc_start: 0.7691 (mtt) cc_final: 0.7350 (mtt) REVERT: B 520 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6759 (mtp-110) REVERT: B 558 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: C 162 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7627 (mtpt) REVERT: D 162 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7427 (mtpt) REVERT: D 179 TRP cc_start: 0.6015 (OUTLIER) cc_final: 0.4827 (t60) REVERT: E 668 GLU cc_start: 0.2478 (OUTLIER) cc_final: 0.1821 (mp0) outliers start: 49 outliers final: 31 residues processed: 145 average time/residue: 0.1796 time to fit residues: 34.7830 Evaluate side-chains 147 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 382 ASN A 385 ASN B 325 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.218237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.190250 restraints weight = 6823.583| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.84 r_work: 0.3926 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.108 Angle : 0.558 6.401 9285 Z= 0.285 Chirality : 0.042 0.154 1080 Planarity : 0.005 0.066 1149 Dihedral : 8.241 57.438 935 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.33 % Favored : 89.54 % Rotamer: Outliers : 6.48 % Allowed : 29.23 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.30), residues: 784 helix: -0.57 (0.30), residues: 289 sheet: -0.44 (0.58), residues: 87 loop : -2.45 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 179 HIS 0.007 0.001 HIS B 430 PHE 0.011 0.001 PHE A 362 TYR 0.011 0.001 TYR B 383 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 168) hydrogen bonds : angle 4.69062 ( 495) covalent geometry : bond 0.00259 ( 6826) covalent geometry : angle 0.55765 ( 9285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7965 (mp10) cc_final: 0.7366 (mt0) REVERT: A 383 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: A 391 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6187 (mmtt) REVERT: A 517 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7273 (tmtt) REVERT: A 519 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7177 (mp) REVERT: A 558 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7025 (ttt90) REVERT: B 339 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: B 369 GLN cc_start: 0.7253 (tt0) cc_final: 0.6988 (mt0) REVERT: B 408 MET cc_start: 0.7706 (mtt) cc_final: 0.7362 (mtt) REVERT: B 520 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6754 (mtp-110) REVERT: B 558 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7109 (ttt90) REVERT: C 150 TRP cc_start: 0.7834 (t-100) cc_final: 0.7141 (t60) REVERT: C 162 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7623 (mtpt) REVERT: D 106 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3342 (pp) REVERT: D 162 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7442 (mtpt) REVERT: D 179 TRP cc_start: 0.5993 (OUTLIER) cc_final: 0.4724 (t60) REVERT: E 668 GLU cc_start: 0.2400 (OUTLIER) cc_final: 0.1780 (mp0) REVERT: F 673 MET cc_start: 0.7000 (mtt) cc_final: 0.6521 (mtt) outliers start: 49 outliers final: 34 residues processed: 142 average time/residue: 0.1872 time to fit residues: 35.4699 Evaluate side-chains 145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 558 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.212379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.185229 restraints weight = 6971.800| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.78 r_work: 0.3867 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6826 Z= 0.194 Angle : 0.669 6.800 9285 Z= 0.337 Chirality : 0.045 0.156 1080 Planarity : 0.006 0.069 1149 Dihedral : 8.503 59.667 935 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.86 % Favored : 88.01 % Rotamer: Outliers : 6.75 % Allowed : 30.03 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.29), residues: 784 helix: -0.97 (0.29), residues: 292 sheet: -0.63 (0.58), residues: 86 loop : -2.59 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 577 HIS 0.007 0.001 HIS B 364 PHE 0.016 0.002 PHE B 434 TYR 0.016 0.002 TYR B 383 ARG 0.006 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 168) hydrogen bonds : angle 4.90308 ( 495) covalent geometry : bond 0.00478 ( 6826) covalent geometry : angle 0.66852 ( 9285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 339 GLN cc_start: 0.8028 (mp10) cc_final: 0.7424 (mt0) REVERT: A 371 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.6099 (tpp) REVERT: A 383 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: A 391 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6355 (mmtt) REVERT: A 517 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7600 (tmtt) REVERT: A 519 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 339 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: B 369 GLN cc_start: 0.7239 (tt0) cc_final: 0.6922 (mt0) REVERT: B 371 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.6490 (tpp) REVERT: B 520 ARG cc_start: 0.7305 (mtm110) cc_final: 0.6873 (mtp-110) REVERT: B 558 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7190 (ttt90) REVERT: C 162 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: D 162 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7544 (mtpt) REVERT: D 179 TRP cc_start: 0.6028 (OUTLIER) cc_final: 0.4770 (t60) REVERT: E 668 GLU cc_start: 0.2727 (OUTLIER) cc_final: 0.2003 (mp0) REVERT: F 643 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.4976 (pp20) REVERT: F 673 MET cc_start: 0.7192 (mtt) cc_final: 0.6655 (mtt) outliers start: 51 outliers final: 32 residues processed: 143 average time/residue: 0.1811 time to fit residues: 34.6835 Evaluate side-chains 144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 385 ASN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.216725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.189786 restraints weight = 6972.605| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.78 r_work: 0.3915 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.117 Angle : 0.574 6.003 9285 Z= 0.295 Chirality : 0.042 0.156 1080 Planarity : 0.006 0.067 1149 Dihedral : 7.890 57.858 931 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.33 % Favored : 89.54 % Rotamer: Outliers : 5.56 % Allowed : 31.61 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.30), residues: 784 helix: -0.56 (0.30), residues: 289 sheet: -0.60 (0.57), residues: 87 loop : -2.48 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 179 HIS 0.005 0.001 HIS B 430 PHE 0.012 0.002 PHE B 362 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 168) hydrogen bonds : angle 4.65256 ( 495) covalent geometry : bond 0.00284 ( 6826) covalent geometry : angle 0.57394 ( 9285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7971 (mp10) cc_final: 0.7371 (mt0) REVERT: A 371 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.6119 (tpp) REVERT: A 383 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: A 391 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6335 (mmtt) REVERT: A 517 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7474 (tmtt) REVERT: A 519 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 339 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: B 369 GLN cc_start: 0.7179 (tt0) cc_final: 0.6862 (mt0) REVERT: B 371 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.6406 (tpp) REVERT: B 408 MET cc_start: 0.7642 (mtt) cc_final: 0.7326 (mtt) REVERT: B 520 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6782 (mtp-110) REVERT: B 558 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7110 (ttt90) REVERT: C 162 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7734 (mtpt) REVERT: D 106 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3329 (pp) REVERT: D 162 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7560 (mtpt) REVERT: D 179 TRP cc_start: 0.6019 (OUTLIER) cc_final: 0.4754 (t60) REVERT: E 668 GLU cc_start: 0.2722 (OUTLIER) cc_final: 0.1998 (mp0) REVERT: F 643 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5082 (pp20) REVERT: F 673 MET cc_start: 0.7219 (mtt) cc_final: 0.6710 (mtt) outliers start: 42 outliers final: 25 residues processed: 139 average time/residue: 0.1927 time to fit residues: 36.0741 Evaluate side-chains 141 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 558 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 66 GLN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 665 LEU Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 665 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 385 ASN D 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.216904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.188046 restraints weight = 6982.804| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.92 r_work: 0.3901 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6826 Z= 0.123 Angle : 0.581 5.746 9285 Z= 0.298 Chirality : 0.043 0.154 1080 Planarity : 0.006 0.070 1149 Dihedral : 7.838 58.023 929 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 5.03 % Allowed : 31.75 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.30), residues: 784 helix: -0.50 (0.30), residues: 289 sheet: -0.59 (0.57), residues: 87 loop : -2.40 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 179 HIS 0.007 0.001 HIS B 430 PHE 0.012 0.002 PHE B 362 TYR 0.012 0.001 TYR A 332 ARG 0.003 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 168) hydrogen bonds : angle 4.64551 ( 495) covalent geometry : bond 0.00301 ( 6826) covalent geometry : angle 0.58077 ( 9285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.98 seconds wall clock time: 58 minutes 20.18 seconds (3500.18 seconds total)